This study was conducted to evaluate the effects of Bradyrhizobium japonicum SAY3-7, Bradyrhizobium elkanii BLY3-8, and Streptomyces griseoflavus P4 on the symbiotic effectiveness of soybeans before biofertilizer production, to produce biofertilizer containing the studied three strains (SAY3-7, BLY3-8, and P4), to test the effectiveness of the biofertilizer on soybean varieties, and to assess the varietal effects and interaction effects between variety and biofertilizer on plant growth, nodulation, nitrogen fixation, nutrient absorption, and seed yield. Nitrogen fixation was measured using the acetylene reduction assay and ureide methods. Contents of nutrients (N, P, K, Ca, and Mg) were also measured to calculate their uptakes. In this study, synergistic effects of nitrogen fixation were induced by combined inoculation with SAY3-7, BLY3-8 and P4 in all tested soybean varieties. Therefore, we assumed that an effective biofertilizer could be produced using these effective bacteria (SAY3-7, BLY3-8, and P4). After making biofertilizer using these effective bacteria, packages were stored at 30 °C. The populations of the bacteria in the biofertilizer were maintained at a density of 1 × 108 colony forming units (cfu) g−1 for P4 and 7 × 109 cells g−1 for Bradyrhizobium. Diluting biofertilizer by 10−3 proved more effective for nodulation and nitrogen fixation than other dilution treatments. Moreover, this biofertilizer significantly promoted plant growth, nodulation, nitrogen fixation, nutrient uptakes, and seed yield in Yezin-3 and Yezin-6 soybean varieties. Yezin-6 is a more efficient variety than Yezin-3 for improved plant growth, nodulation, nitrogen fixation, nutrient absorption, and seed yield. Taken together, the application of an effective biofertilizer and the use of an efficient soybean variety can play important roles in promoting plant growth, nodulation, nitrogen fixation, and higher seed yield.